This is a list of mostly R packages and resources for fisheries. I've included some other materials including publicly available notes on fisheries economics, and some non-R software for fisheries managers as well as other resources.
An introduction to basic fisheries analysis in R (UCSB)
Malcolm Haddon, Using R for Modelling and Quantitative Methods in Fisheries
Arne Eide, Introduction to Fisheries Economics uses Mathematica
my own notes, Notes on the Gordon-Schaefer Model (uses Python)
Notes on Fisheries Economics, Lozada
Rob Hicks IPython notebook on the Gordon-Schaefer Model
The R package kobe This can be now installed via the Fisheries library in R (FLR)
rfisheries access to the Openfisheries.org API This gives access to global fisheries catch and other data.
Generalised Management Strategy Evaluation (GMSE)
PriotizeR Basically a frontend/wrapper for Marxan
BESTMPA Not really maintained anymore which is a pity.
DLMtool: Data-Limited Methods Toolkit
This provides access to the NOAA data API:
Marmap is used for downloading and plotting marine bathymetric and topographic data:
A PlosOne article about marmap marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R
Sea-Py Python oceanographic resources.
List of Python Geo-Spatial resources
OpenFisheries API gives access to FAO FishStatJ data.
Maritime Vehicle Routing Problem Solver
Boatnet a Mobile data collection platform for observers Boatnet (not R but useful)
OPenEM Electronic monitoring software OpenEM
UnionVMS Open source VMS
Vismon Visual Fisheries management and fisheries data analysis and visualization tool.
Focus Fish Open source fisheries resources
Displace GUI based tool to model displacement and movement of fish stocks for spatial fisheries planning and management.
NOAA fisheries Integrated Toolbox
FishNet AI Training datasets for machine learning in fisheries.
Ships in Satellite Imagery (Kaggle) This is a labelled dataset for a Kaggle competition for ship classification. An example of a CNN for this here Towards data science code example
Ram Legacy Stock Assessment Data
FAO Fish Vessel Finder Broken link!
Calfish Fisheries data from California.
Miscellaneous fisheries links on Github